Well... it depends of the level of customization.
First and very important step is backup your template files.If you change css and php files, you need to compare files using any merge software that compares the differences make. I can recommend some (all free and powerful):
WinMergeKdiff3DiffMergeIt will give you some work.
Since there's always updates to considerate, that's why you should use as possible all your css customization on ../css/override.css.
By enabling the use of css override on template parameters > advanced settings.